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Horst B, van Duijnen N, Janssen E, Hansen T, Ruijter E. Modular Divergent Synthesis of Indole Alkaloid Derivatives by an Atypical Ugi Multicomponent Reaction. Chemistry 2024:e202400477. [PMID: 38498145 DOI: 10.1002/chem.202400477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
We present an Ugi multicomponent approach to explore the chemical space around Aspidosperma-type monoterpene indole alkaloids. By variation of the isocyanide and carboxylic acid inputs we demonstrate the rapid generation of molecular diversity and the possibility to introduce handles for further modification. The key Ugi three-component reaction showed full diastereoselectivity towards the cis-fused ring system, which can be rationalized by DFT calculations. Moreover indicating that the reaction proceeds via a Passerini-type hydrogen bonding mechanism. Several post-Ugi modifications were also performed, including Pictet-Spengler cyclization to highly complex nonacyclic natural product hybrid scaffolds.
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Affiliation(s)
- Brendan Horst
- Vrije Universiteit Amsterdam, Chemistry & Pharmaceutical Sciences, NETHERLANDS
| | - Niels van Duijnen
- Vrije Universiteit Amsterdam, Chemistry & Pharmaceutical Sciences, NETHERLANDS
| | - Elwin Janssen
- Vrije Universiteit Amsterdam, Chemistry & Pharmaceutical Sciences, NETHERLANDS
| | - Thomas Hansen
- Vrije Universiteit Amsterdam, Chemistry & Pharmaceutical Sciences, NETHERLANDS
| | - Eelco Ruijter
- Vrije Universiteit Amsterdam, Chemistry & Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Netherlands, 1081 HZ, Amsterdam, NETHERLANDS
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2
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Ávalos G, Caballero-Gómez J, Matas-Méndez P, Castro-Scholten S, Jiménez-Martín D, Köster PC, Santín M, Bailo B, Cano-Terriza D, González-Barrio D, Mateo M, García-Bocanegra I, Dashti A, Nájera F, Carmena D. Detection and genotyping of zoonotic microsporidia in the endangered Iberian lynx (Lynx pardinus). Med Mycol 2024:myae027. [PMID: 38499442 DOI: 10.1093/mmy/myae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024] Open
Abstract
Microsporidia is a diverse group of obligate, intracellular and spore-forming parasites that infect a wide range of animals. Among them, Enterocytozoon bieneusi and Encephalitozoon spp. are the most frequently reported species in humans. Limited information is available about the presence and molecular diversity of microsporidian species in the endangered Iberian lynx (Lynx pardinus). Presence of Enterocytozoon bieneusi and Encephalitozoon spp. was investigated by molecular methods in wild and captive Iberian lynxes from Spain. Overall, E. bieneusi was detected in 3.2% (8/251) of the animals examined. None of the samples tested were positive for Encephalitozoon spp. Four known (D, EbfelA, PigEBITS7, and Type IV) and a novel (named as LynxSpEb1) E. bieneusi genotypes were identified. All the genotypes found belonged to the zoonotic Group 1 of E. bieneusi. This study provides the first genotyping data of E. bieneusi in Iberian lynx in Spain. Our result indicate that the Iberian lynx does not seem to play a relevant role in the epidemiology of Encephalitozoon spp., and that this endangered felid is likely acting as spillover host rather than a true reservoir of E. bieneusi. Additional studies should be conducted to assess the impact of this parasite in the health status of the endangered Iberian lynx.
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Affiliation(s)
- Gabriel Ávalos
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Javier Caballero-Gómez
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emerging Diseases (ENZOEM), University of Córdoba, Córdoba, Spain
- Infectious Diseases Unit, Maimonides Institute for Biomedical Research (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Pablo Matas-Méndez
- Faculty of Veterinary, Alfonso X El Sabio University (UAX), Villanueva de la Cañada, Madrid, Spain
| | - Sabrina Castro-Scholten
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emerging Diseases (ENZOEM), University of Córdoba, Córdoba, Spain
| | - Débora Jiménez-Martín
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emerging Diseases (ENZOEM), University of Córdoba, Córdoba, Spain
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
- Women for Africa Foundation, Madrid, Spain
| | - Mónica Santín
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - David Cano-Terriza
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emerging Diseases (ENZOEM), University of Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Marta Mateo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Ignacio García-Bocanegra
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emerging Diseases (ENZOEM), University of Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Fernando Nájera
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
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3
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Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024; 43:113857. [PMID: 38421866 DOI: 10.1016/j.celrep.2024.113857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generate a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database. Single-cell RNA sequencing of 13,200 cells reveals that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. Extending C. elegans Neuronal Gene Expression Map and Network (CeNGEN) findings, all MN subclasses are delineated by distinct expression codes of either neuropeptide or transcription factor gene families. Strikingly, combinatorial codes of homeodomain transcription factor genes succinctly delineate adult MN diversity in both C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Rebecca Collings
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Program in Neuroscience, Vanderbilt University, Nashville, TN 37240, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA.
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4
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Beato A, Haudecoeur R, Boucherle B, Peuchmaur M. Expanding Chemical Frontiers: Approaches for Generating Diverse and Bioactive Natural Product-Like Compounds Libraries from Extracts. Chemistry 2024:e202304166. [PMID: 38372433 DOI: 10.1002/chem.202304166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
The realms of natural products and synthetic compounds exhibit distinct chemical spaces that not only differ but also complement each other. While the convergence of these two domains has been explored through semisynthesis and conventional pharmacomodulation endeavours applied to natural frameworks, a recent and innovative approach has emerged that involves the combinatorial generation of libraries of 'natural product-like compounds' (NPLCs) through the direct synthetic derivatization of natural extracts. This has led to the production of numerous NPLCs that incorporate structural elements from both their natural (multiple saturated rings, oxygen content, chiral centres) and synthetic (aromatic rings, nitrogen and halogen content, drug-like properties) precursors. Through careful selection of extracts and reagents, specific bioactivities have been achieved, and this strategy has been deployed in various ways, showing great promise without reaching its full potential to date. This review seeks to provide an overview of reported examples involving the chemical engineering of extracts, showcasing a spectrum of natural product alterations spanning from simple substitutions to complete scaffold remodelling. It also includes an analysis of the accomplishments, perspectives and technical challenges within this field.
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Affiliation(s)
- Aurélien Beato
- Univ. Grenoble Alpes, CNRS, DPM, Bâtiment E Pôle Chimie BP 53, 38000, Grenoble, France
| | - Romain Haudecoeur
- Univ. Grenoble Alpes, CNRS, DPM, Bâtiment E Pôle Chimie BP 53, 38000, Grenoble, France
| | - Benjamin Boucherle
- Univ. Grenoble Alpes, CNRS, DPM, Bâtiment E Pôle Chimie BP 53, 38000, Grenoble, France
| | - Marine Peuchmaur
- Univ. Grenoble Alpes, CNRS, DPM, Bâtiment E Pôle Chimie BP 53, 38000, Grenoble, France
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5
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Deska-Gauthier D, Borowska-Fielding J, Jones C, Zhang H, MacKay CS, Michail R, Bennett LA, Bikoff JB, Zhang Y. Embryonic temporal-spatial delineation of excitatory spinal V3 interneuron diversity. Cell Rep 2024; 43:113635. [PMID: 38160393 PMCID: PMC10877927 DOI: 10.1016/j.celrep.2023.113635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Spinal neural circuits that execute movement are composed of cardinal classes of neurons that emerged from distinct progenitor lineages. Each cardinal class contains multiple neuronal subtypes characterized by distinct molecular, anatomical, and physiological characteristics. Through a focus on the excitatory V3 interneuron class, here we demonstrate that interneuron subtype diversity is delineated through a combination of neurogenesis timing and final laminar settling position. We have revealed that early-born and late-born embryonic V3 temporal classes further diversify into subclasses with spatially and molecularly discrete identities. While neurogenesis timing accounts for V3 morphological diversification, laminar settling position accounts for electrophysiological profiles distinguishing V3 subtypes within the same temporal classes. Furthermore, V3 interneuron subtypes display independent behavioral recruitment patterns demonstrating a functional modularity underlying V3 interneuron diversity. These studies provide a framework for how early embryonic temporal and spatial mechanisms combine to delineate spinal interneuron classes into molecularly, anatomically, and functionally relevant subtypes in adults.
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Affiliation(s)
- Dylan Deska-Gauthier
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Joanna Borowska-Fielding
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chris Jones
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Han Zhang
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Colin S MacKay
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ramez Michail
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Laura A Bennett
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ying Zhang
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Potapova NA, Zlobin AS, Perfil’ev RN, Vasiliev GV, Salina EA, Tsepilov YA. Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia. Plants (Basel) 2023; 12:3490. [PMID: 37836230 PMCID: PMC10575349 DOI: 10.3390/plants12193490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Soybean is a leguminous plant cultivated in many countries and is considered important in the food industry due to the high levels of oil and protein content in the beans. The high demand for soybeans and its products in the industry requires the expansion of cultivation areas. Despite climatic restrictions, West Siberia is gradually expanding its area of soybean cultivation. In this study, we present the first analysis of the population structure and genetic diversity of the 175 soybean Glycine max breeding lines and varieties cultivated in West Siberia (103 accessions) and other regions of Russia (72 accessions), and we compare them with the cultivated soybean varieties from other geographical locations. Principal component analysis revealed several genetic clusters with different levels of genetic heterogeneity. Studied accessions are genetically similar to varieties from China, Japan, and the USA and are genetically distant to varieties from South Korea. Admixture analysis revealed four ancestry groups based on genetic ancestry and geographical origin, which are consistent with the regions of cultivation and origin of accessions and correspond to the principal component analysis result. Population statistics, including nucleotide diversity, Tajima's D, and linkage disequilibrium, are comparatively similar to those observed for studied accessions of a different origin. This study provides essential population and genetic information about the unique collection of breeding lines and varieties cultivated in West Siberia and other Russian regions to foster further evolutionary, genome-wide associations and functional breeding studies.
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Affiliation(s)
- Nadezhda A. Potapova
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, 127051 Moscow, Russia
| | - Alexander S. Zlobin
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Roman N. Perfil’ev
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Gennady V. Vasiliev
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena A. Salina
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Yakov A. Tsepilov
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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Ginex T, Madruga E, Martinez A, Gil C. MBC and ECBL libraries: outstanding tools for drug discovery. Front Pharmacol 2023; 14:1244317. [PMID: 37637414 PMCID: PMC10457160 DOI: 10.3389/fphar.2023.1244317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
Chemical libraries have become of utmost importance to boost drug discovery processes. It is widely accepted that the quality of a chemical library depends, among others, on its availability and chemical diversity which help in rising the chances of finding good hits. In this regard, our group has developed a source for useful chemicals named Medicinal and Biological Chemistry (MBC) library. It originates from more than 30 years of experience in drug design and discovery of our research group and has successfully provided effective hits for neurological, neurodegenerative and infectious diseases. Moreover, in the last years, the European research infrastructure for chemical biology EU-OPENSCREEN has generated the European Chemical Biology library (ECBL) to be used as a source of hits for drug discovery. Here we present and discuss the updated version of the MBC library (MBC v.2022), enriched with new scaffolds and containing more than 2,500 compounds together with ECBL that collects about 100,000 small molecules. To properly address the improved potentialities of the new version of our MBC library in drug discovery, up to 44 among physicochemical and pharmaceutical properties have been calculated and compared with those of other well-known publicly available libraries. For comparison, we have used ZINC20, DrugBank, ChEMBL library, ECBL and NuBBE along with an approved drug library. Final results allowed to confirm the competitive chemical space covered by MBC v.2022 and ECBL together with suitable drug-like properties. In all, we can affirm that these two libraries represent an interesting source of new hits for drug discovery.
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Affiliation(s)
- Tiziana Ginex
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB-CSIC), Madrid, Spain
| | - Enrique Madruga
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB-CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB-CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Gil
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB-CSIC), Madrid, Spain
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Li F, Tang S, Lv J, He A, Wang Y, Liu S, Cao H, Zhao L, Wang Y, Jiang G. Molecular-Scale Investigation on the Formation of Brown Carbon Aerosol via Iron-Phenolic Compound Reactions in the Dark. Environ Sci Technol 2023; 57:11173-11184. [PMID: 37462533 DOI: 10.1021/acs.est.3c04263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Brown carbon (BrC) is one of the most mysterious aerosol components responsible for global warming and air pollution. Iron (Fe)-induced catalytic oxidation of ubiquitous phenolic compounds has been considered as a potential pathway for BrC formation in the dark. However, the reaction mechanism and product composition are still poorly understood. Herein, 13 phenolic precursors were employed to react with Fe under environmentally relevant conditions. Using Fourier transform ion cyclotron resonance mass spectrometry, a total of 764 unique molecular formulas were identified, and over 85% of them can be found in atmospheric aerosols. In particular, products derived from precursors with catechol-, guaiacol-, and syringol-like-based structures can be distinguished by their optical and molecular characteristics, indicating the structure-dependent formation of BrC from phenolic precursors. Multiple pieces of evidence indicate that under acidic conditions, the contribution of either autoxidation or oxygen-induced free radical oxidation to BrC formation is extremely limited. Ligand-to-Fe charge transfer and subsequent phenoxy radical coupling reactions were the main mechanism for the formation of polymerization products with high molecular diversity, and the efficiency of BrC generation was linearly correlated with the ionization potential of phenolic precursors. The present study uncovered how chemically diverse BrC products were formed by the Fe-phenolic compound reactions at the molecular level and also provide a new paradigm for the study of the atmospheric aerosol formation mechanism.
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Affiliation(s)
- Feifei Li
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Tang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jitao Lv
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anen He
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yarui Wang
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuting Liu
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiming Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Lixia Zhao
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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9
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Davenport R, Bowen BP, Lynch LM, Kosina SM, Shabtai I, Northen TR, Lehmann J. Decomposition decreases molecular diversity and ecosystem similarity of soil organic matter. Proc Natl Acad Sci U S A 2023; 120:e2303335120. [PMID: 37307452 DOI: 10.1073/pnas.2303335120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 06/14/2023] Open
Abstract
Soil organic matter (SOM) is comprised of a diverse array of reactive carbon molecules, including hydrophilic and hydrophobic compounds, that impact rates of SOM formation and persistence. Despite clear importance to ecosystem science, little is known about broad-scale controls on SOM diversity and variability in soil. Here, we show that microbial decomposition drives significant variability in the molecular richness and diversity of SOM between soil horizons and across a continental-scale gradient in climate and ecosystem type (arid shrubs, coniferous, deciduous, and mixed forests, grasslands, and tundra sedges). The molecular dissimilarity of SOM was strongly influenced by ecosystem type (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 10% P < 0.001) and soil horizon (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 21%, P < 0.001), as assessed using metabolomic analysis of hydrophilic and hydrophobic metabolites. While the proportion of shared molecular features was significantly higher in the litter layer than subsoil C horizons across ecosystems (12 times and 4 times higher for hydrophilic and hydrophobic compounds, respectively), the proportion of site-specific molecular features nearly doubled from the litter layer to the subsoil horizon, suggesting greater differentiation of compounds after microbial decomposition within each ecosystem. Together, these results suggest that microbial decomposition of plant litter leads to a decrease in SOM α-molecular diversity, yet an increase in β-molecular diversity across ecosystems. The degree of microbial degradation, determined by the position in the soil profile, exerts a greater control on SOM molecular diversity than environmental factors, such as soil texture, moisture, and ecosystem type.
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Affiliation(s)
- Rachelle Davenport
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Metabolomics Technology Group Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598
| | - Laurel M Lynch
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Itamar Shabtai
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Metabolomics Technology Group Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850
- Department of Global Development, Cornell University, Ithaca, NY 14850
- Cornell Institute for Digital Agriculture, Cornell University, Ithaca, NY 14850
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14850
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10
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Song F, Li T, Wu F, Leung KMY, Hur J, Zhou L, Bai Y, Zhao X, He W, Ruan M. Temperature-Dependent Molecular Evolution of Biochar-Derived Dissolved Black Carbon and Its Interaction Mechanism with Polyvinyl Chloride Microplastics. Environ Sci Technol 2023; 57:7285-7297. [PMID: 37098046 DOI: 10.1021/acs.est.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Biochar-derived dissolved black carbon (DBC) molecules are dependent on the BC formation temperature and affect the fate of emerging contaminants in waters, such as polyvinyl chloride microplastic (MPPVC). However, the temperature-dependent evolution and MPPVC-interaction of DBC molecules remain unclear. Herein, we propose a novel DBC-MPPVC interaction mechanism by systematically interpreting heterogeneous correlations, sequential responses, and synergistic relationships of thousands of molecules and their linking functional groups. Two-dimensional correlation spectroscopy was proposed to combine Fourier transform-ion cyclotron resonance mass spectrometry and spectroscopic datasets. Increased temperature caused diverse DBC molecules and fluorophores, accompanied by molecular transformation from saturation/reduction to unsaturation/oxidation with high carbon oxidation states, especially for molecules with acidic functional groups. The temperature response of DBC molecules detected via negative-/positive-ion electrospray ionization sequentially occurred in unsaturated hydrocarbons → lignin-like → condensed aromatic → lipid-/aliphatic-/peptide-like → tannin-like → carbohydrate-like molecules. DBC molecular changes induced by temperature and MPPVC interaction were closely coordinated, with lignin-like molecules contributing the most to the interaction. Functional groups in DBC molecules with m/z < 500 showed a sequential MPPVC-interaction response of phenol/aromatic ether C-O, alkene C═C/amide C═O → polysaccharides C-O → alcohol/ether/carbohydrate C-O groups. These findings help to elucidate the critical role of DBCs in MP environmental behaviors.
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Affiliation(s)
- Fanhao Song
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tingting Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kenneth Mei Yee Leung
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Jin Hur
- Department of Environment and Energy, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea
| | - Lingfeng Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wei He
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Mingqi Ruan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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11
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Okolo EA, Pahl A, Sievers S, Pask CM, Nelson A, Marsden SP. Scaffold Remodelling of Diazaspirotricycles Enables Synthesis of Diverse sp 3 -Rich Compounds With Distinct Phenotypic Effects. Chemistry 2023; 29:e202203992. [PMID: 36722618 PMCID: PMC10946999 DOI: 10.1002/chem.202203992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A 'top down' scaffold remodelling approach to library synthesis was applied to spirotricyclic ureas prepared by a complexity-generating oxidative dearomatisation. Eighteen structurally-distinct, sp3 -rich scaffolds were accessed from the parent tricycle through ring addition, cleavage and expansion strategies. Biological screening of a small compound library based on these scaffolds using the cell-painting assay demonstrated distinctive phenotypic responses engendered by different library members, illustrating the functional as well as structural diversity of the compounds.
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Affiliation(s)
| | - Axel Pahl
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Sonja Sievers
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | | | - Adam Nelson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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12
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Wang X, Wang W, Qin Y, Wang M, Li Y, Liu H. Population Genetic Diversity of Two Blue Oat Mite Species on Triticum Hosts in China. Insects 2023; 14:377. [PMID: 37103192 PMCID: PMC10143575 DOI: 10.3390/insects14040377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Blue oat mite species, including Penthaleus major and P. tectus, are pests widely distributed across China that cause damage to winter wheat. This study evaluated the genetic diversity of P. major and P. tectus on Triticum hosts collected from 23 geographic locations based on mitochondrial cytochrome c oxidase subunit I (COI) sequences. We identified nine haplotypes in 438 P. major individuals from 21 geographic locations and five haplotypes in 139 P. tectus individuals from 11 geographic locations. Meanwhile, P. major exhibits high values of haplotype diversity (Hd) and nucleotide diversity (Pi) (Hd = 0.534 > 0.5 and Pi = 0.012 > 0.005), representing a large stable population with a long evolutionary history. P. tectus shows low values of Hd and Pi (Hd = 0.112 < 0.5 and Pi = 0 < 0.005), which suggest recent founder events. Moreover, demographic analysis suggested that P. major and P. tectus have not undergone a recent population expansion. The lowest genetic variation was observed in Xiangzhou (XZ-HB), Zaoyang (ZY-HB), Siyang (SY-JS), and Rongxian (RX-SC), with only one species and one haplotype identified in over 30 individuals. Robust genetic differentiation was found in P. major compared to P. tectus, which provides a theoretical basis for the widespread distribution of P. major in China.
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13
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Chozas M, Dashti A, Prieto-Pérez L, Pérez-Tanoira R, Cobo E, Bailo B, Del Palacio M, Hernández-Castro C, González-Barrio D, Carmena D, Köster PC. Enterocytozoon bieneusi and Encephalitozoon intestinalis (Microsporidia) in HIV-positive patients in central Spain. Med Mycol 2023; 61:7110408. [PMID: 37024274 DOI: 10.1093/mmy/myad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023] Open
Abstract
Microsporidia are fungi-related eukaryotic intracellular parasites that opportunistically infect immunocompromised individuals such as those infected by the human immunodeficiency virus (HIV). Among them, Enterocytozoon bieneusi and Encephalitozoon spp. are the most clinically relevant species. We investigated the occurrence and genetic diversity of microsporidial and protist infections in mostly immunocompetent HIV-positive patients in Madrid, Spain. A structured questionnaire was used to retrieve data on factors potentially associated with an increased risk of infection, including sexual attitudes and sex-risk behaviour. Faecal samples (n = 96) from 81 HIV-positive patients were collected and analysed by molecular (PCR and Sanger sequencing) methods. Two microsporidial pathogens were detected including E. bieneusi (2.5%, 95% CI: 0.3-8.6) and E. intestinalis (4.9%, 95% CI: 1.4-12.2). The two E. bieneusi isolates were identified as zoonotic genotype A. Among protists, Entamoeba dispar was the species most prevalently found (33.3%, 95% CI: 23.2-44.7), followed by Blastocystis sp. (19.8%, 95% CI: 11.7-30.1), Giardia duodenalis (13.6%, 95% CI: 7.0-23.0), and Cryptosporidium spp. and Entamoeba histolytica (2.5%, 95% CI: 0.3-8.6 each). Cyclospora cayetanensis and Cystoisospora belli were not detected. Subtypes ST1 (70.6%, 12/17) and ST3 (29.4%, 5/17) were identified within Blastocystis sp., sub-assemblages AII and BIII (50%, 1/2 each) within G. duodenalis, and C. parvum and canine-adapted C. canis (50%, 1/2 each) within Cryptosporidium spp. Microsporidial and protist parasites were frequent in well-controlled, mostly immunocompetent HIV-positive patients and should be included in diagnostic algorithms when diarrhoea is present.
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Affiliation(s)
- Mercedes Chozas
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Laura Prieto-Pérez
- Department of Internal Medicine and Infectious Diseases, University Hospital Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Ramón Pérez-Tanoira
- Department of Clinical Microbiology, University Hospital Príncipe de Asturias, Meco, 28805 Madrid, Spain
- Department of Biomedicine and Biotechnology, Faculty of Medicine, Alcalá de Henares University, 28871 Alcalá de Henares, Spain
| | - Elena Cobo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Marta Del Palacio
- Department of Internal Medicine and Infectious Diseases, University Hospital Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Carolina Hernández-Castro
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
- Centre for Biomedical Research Network (CIBER) in Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
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14
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Figueiredo AM, Dashti A, Santín M, Köster PC, Torres RT, Fonseca C, Mysterud A, Carvalho J, Sarmento P, Neves N, Hipólito D, Palmeira JD, Teixeira D, Lima C, Calero-Bernal R, Carmena D. Occurrence and molecular characterization of Enterocytozoon bieneusi in wild and domestic animal species in Portugal. Med Mycol 2023; 61:7028777. [PMID: 36746434 DOI: 10.1093/mmy/myad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.
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Affiliation(s)
- Ana M Figueiredo
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Centre for Ecological and Evolutionary Synthesis, Department of Bioscience, University of Oslo, P.O Box 1066 Blindern, NO-316 Oslo, Norway
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Majadahonda, 28220 Madrid, Spain
| | - Mónica Santín
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Majadahonda, 28220 Madrid, Spain
| | - Rita T Torres
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis, Department of Bioscience, University of Oslo, P.O Box 1066 Blindern, NO-316 Oslo, Norway
| | - João Carvalho
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Sarmento
- Instituto da Conservação da Natureza e das Florestas. Direção Regional do Alentejo. Centro Polivalente da Casa do Lanternim. Rua D. Sancho II, n15 7750-350 Mértola, Portugal
| | - Nuno Neves
- Instituto da Conservação da Natureza e das Florestas. Direção Regional do Alentejo. Centro Polivalente da Casa do Lanternim. Rua D. Sancho II, n15 7750-350 Mértola, Portugal
| | - Dário Hipólito
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Josman D Palmeira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Daniela Teixeira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Lima
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rafael Calero-Bernal
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Majadahonda, 28220 Madrid, Spain.,CIBER Infectious Diseases (CIBERINFEC), Health Institute Carlos III, 28029 Madrid, Spain
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15
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Cavadas J, Parreira R, Leonardo I, Barreto Crespo MT, Nunes M. Mastadenovirus Molecular Diversity in Waste and Environmental Waters from the Lisbon Metropolitan Area. Microorganisms 2022; 10:microorganisms10122443. [PMID: 36557697 PMCID: PMC9783802 DOI: 10.3390/microorganisms10122443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
In face of the absence of epidemiological data regarding the circulation of human adenoviruses (HAdV) in Portugal, this study aimed at the evaluation of their molecular diversity in waste and environmental waters in the Lisbon Metropolitan Area (LMA). Using samples collected between 2018 and 2021, the HAdV hexon protein-coding sequence was partially amplified using three nested touch-down PCR protocols. The amplification products obtained were analyzed in parallel by two approaches: molecular cloning followed by Sanger sequencing and Next-Generation Sequencing (NGS) using Illumina® sequencing. The analysis of NGS-generated data allowed the identification of a higher diversity of HAdV-A (19%), -B (1%), -C (3%), -D (24%), and -F (25%) viral types, along with murine adenovirus (MAdV-2; 30%) in the wastewater treatment plant samples. On the other hand, HAdV-A (19%), -D (32%), and -F (36%) were identified in environmental samples, and possibly MAdV-2 (14%). These results demonstrate the presence of fecal contamination in environmental waters and the assessment of the diversity of this virus provides important information regarding the distribution of HAdV in LMA, including the detection of HAdV-F41, the most frequently reported in water worldwide.
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Affiliation(s)
- Joana Cavadas
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2781-901 Oeiras, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Rua da Junqueira No. 100, 1349-008 Lisboa, Portugal
- Global Health and Tropical Medicine (GHTM) Research Centre, 1349-008 Lisboa, Portugal
| | - Inês Leonardo
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Maria Teresa Barreto Crespo
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Mónica Nunes
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (NOVA), Av. da República, 2780-157 Oeiras, Portugal
- Correspondence: ; Tel.: +351-21-750-0006 (ext. 20134)
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16
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Ikuta N, Fonseca ASK, Fernando FS, Filho TF, Martins NRDS, Lunge VR. Emergence and molecular characterization of the avian infectious bronchitis virus GI-23 in commercial broiler farms from South America. Transbound Emerg Dis 2022; 69:3167-3172. [PMID: 36197069 DOI: 10.1111/tbed.14724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 02/07/2023]
Abstract
Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease in the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many genetic types, and lineages are described worldwide. IBV genetic type I-strain 23 (GI-23) has spread across different continents (including Asia, Europe and Africa), causing multiple outbreaks and severe economic losses throughout the poultry industry in the last decade. The present study aimed to report the emergence and molecular characterization of GI-23 in South Brazil, being detected for the first time in South America. Eighty-two broiler flocks presenting clinical suspicion of infectious bronchitis were selected for this study. Tracheal, renal and intestinal samples were collected for IBV detection and genotyping. A total of 57 flocks were positive for IBV by generic RT-qPCR targeting 5' untranslated region and 31 also tested positive for GI-11 by a specific RT-qPCR targeting S1 gene for this lineage. The remaining 26 IBV-positive samples were genotyped by partial and one by complete S1 gene/protein sequencing. Phylogenetic analysis demonstrated that all of them clustered into a specific branch of the GI-23. S1 protein sequence analysis evidenced that all Brazilian GI-23 IBVs had the two characteristic amino acid substitutions A93T and S/H118P/L, but other changes were also observed, such as S37F (n = 21; 81%), G117S (n = 17, 65%), P122S (n = 16; 61%) and W71R (n = 9; 35%). This study brings new insights into the epidemiology of the IBV GI-23 in the world, highlighting its emergence and molecular characteristics in Brazil, South America.
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Affiliation(s)
- Nilo Ikuta
- Simbios Biotecnologia, Cachoeirinha, Brazil
| | | | | | - Tobias Fernandes Filho
- Boehringer Ingelheim Animal Health do Brasil, São Paulo, Brazil.,Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | | | - Vagner Ricardo Lunge
- Simbios Biotecnologia, Cachoeirinha, Brazil.,Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul - UCS, Caxias do Sul, Brazil
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17
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Lv J, Huang Z, Luo L, Zhang S, Wang Y. Advances in Molecular and Microscale Characterization of Soil Organic Matter: Current Limitations and Future Prospects. Environ Sci Technol 2022; 56:12793-12810. [PMID: 36037253 DOI: 10.1021/acs.est.2c00421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soil organic matter (SOM) comprises a continuum of organic materials from granular organic debris to small organic molecules and contains more organic carbon than global vegetation and the atmosphere combined. It has remarkable effects on soil ecological functions and the global carbon cycle as well as the fate of pollutants in the terrestrial ecosystem. Therefore, characterization of SOM is an important topic in soil science, ecology, and environmental science. Chemical complexity and spatial heterogeneity are by far the two biggest challenges to our understanding of SOM. Recent developments in analytical techniques and methods provide the opportunity to reveal SOM composition at the molecular level and to observe its distribution in soils at micro- and nanoscales, which have greatly improved our understanding of SOM. This paper reviews the outstanding advances in SOM characterization regarding these two issues from target and nontarget analyses comprising molecular marker analysis, ultrahigh-resolution mass spectrometry analysis, and in situ microscopic imaging techniques such as synchrotron-based spectromicroscopy, nanoscale secondary ion mass spectrometry, and emerging electron and optical microscopic imaging techniques. However, current techniques and methods remain far from unlocking the unknown properties of SOM. We systematically point out the limitations of the current technologies and outline the future prospects for comprehensive characterization of SOM at the molecular level and micro- and nanoscales, paying particular attention to issues of environmental concern.
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Affiliation(s)
- Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoquan Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Guangdong Key Laboratory of Contaminated Site Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, Guangdong 510045, China
| | - Lei Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Dashti A, Santín M, Köster PC, Bailo B, Ortega S, Imaña E, Habela MÁ, Rivero-Juarez A, Vicente J, Arnal MC, de Luco DF, Morrondo P, Armenteros JA, Balseiro A, Cardona GA, Martínez-Carrasco C, Ortiz JA, Calero-Bernal R, Carmena D, González-Barrio D. Zoonotic Enterocytozoon bieneusi genotypes in free-ranging and farmed wild ungulates in Spain. Med Mycol 2022; 60:6696380. [PMID: 36095135 DOI: 10.1093/mmy/myac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/06/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microsporidia comprises a diverse group of obligate, intracellular, and spore-forming parasites that infect a wide range of animals. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and other mammals and birds. Data on the epidemiology of E. bieneusi in wildlife is limited. Hence, E. bieneusi was investigated in eight wild ungulate species present in Spain (genera Ammotragus, Capra, Capreolus, Cervus, Dama, Ovis, Rupicapra, and Sus) by molecular methods. Faecal samples were collected from free-ranging (n = 1058) and farmed (n = 324) wild ungulates from five Spanish bioregions. The parasite was detected only in red deer (10.4%, 68/653) and wild boar (0.8%, 3/359). Enterocytozoon bieneusi infections were more common in farmed (19.4%, 63/324) than in wild (1.5%, 5/329) red deer. Eleven genotypes were identified in red deer, eight known (BEB6, BEB17, EbCar2, HLJD-V, MWC_d1, S5, Type IV, and Wildboar3) and three novel (DeerSpEb1, DeerSpEb2, and DeerSpEb3) genotypes. Mixed genotype infections were detected in 15.9% of farmed red deer. Two genotypes were identified in wild boar, a known (Wildboar3) and a novel (WildboarSpEb1) genotypes. All genotypes identified belonged to E. bieneusi zoonotic Groups 1 and 2. This study provides the most comprehensive epidemiological study of E. bieneusi in Spanish ungulates to date, representing the first evidence of the parasite in wild red deer populations worldwide. Spanish wild boars and red deer are reservoir of zoonotic genotypes of E. bieneusi and might play an underestimated role in the transmission of this microsporidian species to humans and other animals.
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Affiliation(s)
- Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Santín
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Sheila Ortega
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Elena Imaña
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Miguel Ángel Habela
- Department of Animal Health, Veterinary Sciences Faculty, Extremadura University, Caceres, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit, Maimonides Institute for Biomedical Research (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Córdoba, Spain
| | - Joaquin Vicente
- SaBio Group, Institute for Game and Wildlife Research, IREC (UCLM-CSIC-JCCM), Ciudad Real, Spain
| | | | - Maria C Arnal
- Department of Animal Pathology, Veterinary Faculty, University of Zaragoza, Zaragoza, Spain
| | | | - Patrocinio Morrondo
- INVESAGA Group, Department of Animal Pathology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - José A Armenteros
- Council of Development, Territory Planning and the Environment of the Principado de Asturias, Oviedo, Spain
| | - Ana Balseiro
- Animal Health Department, Veterinary School, University of León, León, Spain.,Animal Health Department, Mountain Livestock Institute (CSIC-University of León), León, Spain
| | | | - Carlos Martínez-Carrasco
- Animal Health Department, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", Espinardo, Murcia, Spain
| | - José Antonio Ortiz
- Medianilla S.L., Department of Veterinary and Research. Benalup-Casas Viejas, Spain
| | - Rafael Calero-Bernal
- SALUVET, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
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Al Salameen F, Habibi N, Al Amad S, Al Doaij B. Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS. Plants (Basel) 2022; 11:1435. [PMID: 35684208 PMCID: PMC9183190 DOI: 10.3390/plants11111435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Natural populations of Rhanterium eppaposum Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local Rhanterium plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of Rhanterium. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (FST = 0.029; p = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel's test returned a very weak correlation coefficient of r2 = 0.101 (p = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation.
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Munda S, Saikia RJ, Begum T, Bhandari S, Gogoi A, Sarma N, Tamang R, Lal M. Evaluation of Genetic Diversity Based on Microsatellites and Phytochemical Markers of Core Collection of Cymbopogon winterianus Jowitt Germplasm. Plants (Basel) 2022; 11:528. [PMID: 35214861 PMCID: PMC8878620 DOI: 10.3390/plants11040528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Cymbopogon winterianus Jowitt is an industrially important crop due to its value in the aromatic, perfumery and pharmaceutical industries. In this study, 72 accessions of C. winterianus were selected for molecular diversity analysis using SSR markers. It revealed a total of 65 polymorphic alleles showing an average of 68.10% polymorphism. The best SSR primer with competency in discriminating the germplasm was 3CM0506 with PIC (0.69), MI (0.69) and Rp (3.12). Genetic variation was studied between Assam, Manipur, Meghalaya and Arunachal Pradesh populations. A dendrogram based on the Neighbour-Joining Method showed clustering of germplasm on the collection site. A total of six relevant genetic populations were identified through a structure harvester software analysis. Moreover, a dendrogram based on similarity, complete linkage and Euclidean distance was also elucidated differentiating the genotypes with respect to the major phytochemical constituents of the essential oil. GC-FID and GC-MS analyses of the essential oil of the 72 germplasms revealed citronellal content from 2.58-51.45%, citronellol from 0.00-26.39% and geraniol from 0.00-41.15%. This is the first molecular diversity report with 72 accessions of C. winterianus collected from the NE region using 28 SSR primers as well as their diversity based on phytochemical markers. This diversity computation will help with acquisition of the knowledge and relationship among each individual accession leading to the development of improved and essential oil component-rich cultivars.
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Affiliation(s)
- Sunita Munda
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Raktim Jyoti Saikia
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
| | - Twahira Begum
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Sangeeta Bhandari
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
| | - Ankita Gogoi
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
| | - Neelav Sarma
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Raghu Tamang
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
| | - Mohan Lal
- CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; (S.M.); (R.J.S.); (T.B.); (S.B.); (A.G.); (N.S.); (R.T.)
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
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21
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Townley C, McMurray L, Marsden SP, Nelson A. A unified "top-down" approach for the synthesis of diverse lead-like molecular scaffolds. Bioorg Med Chem Lett 2022; 62:128631. [PMID: 35181466 DOI: 10.1016/j.bmcl.2022.128631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022]
Abstract
A "top-down" synthetic approach enabled the step-efficient synthesis of 21 diverse novel molecular scaffolds. The scaffolds were derived from four complex intermediates that had been prepared using cycloaddition chemistry. Scaffold-hopping of these intermediates was achieved through attachment of an additional ring, ring cleavage, ring expansion and/or ring fusion. It was shown that the resulting scaffolds could be decorated to yield diverse lead-like screening compounds.
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Affiliation(s)
- Chloe Townley
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Lindsay McMurray
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Stephen P Marsden
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
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22
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Piras P. New mathematical measures for apprehending complexity of chiral molecules using information entropy. Chirality 2022; 34:646-666. [PMID: 35146805 DOI: 10.1002/chir.23423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/02/2022] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
In this paper, we present several new theoretical measures based on information entropy that can be used to analyze the information content of a chiral molecule. Starting from a differentiation between "chiral" and "achiral" portions in a chiral molecule, we define a new concept that allows us to quantify the complexity of chiral constitutional 2D-isomers of C10 to C20 alkanes. Various new chiral and achiral information measures founded on joint entropy, mutual information, and conditional entropy are presented providing an access to a set of regression equations. Then, introducing a case-based measure of entropy, we demonstrate that the distribution of the chiral complexity in these molecules is mostly skewed-right: 60% of the chiral isomers follow a 60/40 distribution rule, which indicates a concentration of chiral complexity in a small number of topological features. Furthermore, by replacing 2D topological distances by 3D distances, the application of these new information measures goes from conformational to racemization and deracemization studies. Interestingly, when the geometrical distances between atoms and the chiral center(s) are taken into account when determining the chiral information entropy, one can observe a significative Pearson correlation coefficient (R = 0.70) between the chiral entropy of 3D molecules and the continuous chirality measure. Finally, we show that our approach is applicable to almost any type of chiral organic chemical structures if in the entropy equation, atoms are represented by their electrotopological state (E-state) index instead of connectivity.
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Affiliation(s)
- Patrick Piras
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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Mapps AA, Thomsen MB, Boehm E, Zhao H, Hattar S, Kuruvilla R. Diversity of satellite glia in sympathetic and sensory ganglia. Cell Rep 2022; 38:110328. [PMID: 35108545 DOI: 10.1016/j.celrep.2022.110328] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Satellite glia are the major glial type found in sympathetic and sensory ganglia in the peripheral nervous system, and specifically, contact neuronal cell bodies. Sympathetic and sensory neurons differ in morphological, molecular, and electrophysiological properties. However, the molecular diversity of the associated satellite glial cells remains unclear. Here, using single-cell RNA sequencing analysis, we identify five different populations of satellite glia from sympathetic and sensory ganglia. We define three shared populations of satellite glia enriched in immune-response genes, immediate-early genes, and ion channels/ECM-interactors, respectively. Sensory- and sympathetic-specific satellite glia are differentially enriched for modulators of lipid synthesis and metabolism. Sensory glia are also specifically enriched for genes involved in glutamate turnover. Furthermore, satellite glia and Schwann cells can be distinguished by unique transcriptional signatures. This study reveals the remarkable heterogeneity of satellite glia in the peripheral nervous system.
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Affiliation(s)
- Aurelia A Mapps
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, 200 Mudd Hall, Baltimore, MD 21218, USA
| | - Michael B Thomsen
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, 200 Mudd Hall, Baltimore, MD 21218, USA; Section on Light and Circadian Rhythms (SLCR), National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Erica Boehm
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, 200 Mudd Hall, Baltimore, MD 21218, USA
| | - Haiqing Zhao
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, 200 Mudd Hall, Baltimore, MD 21218, USA
| | - Samer Hattar
- Section on Light and Circadian Rhythms (SLCR), National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Rejji Kuruvilla
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, 200 Mudd Hall, Baltimore, MD 21218, USA.
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Xue L, Khan MH, Yue J, Zhu Z, Niu L. The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns. J Biol Chem 2021; 298:101457. [PMID: 34861238 PMCID: PMC8717551 DOI: 10.1016/j.jbc.2021.101457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous regulatory modules for bacterial growth and cell survival following stress. YefM-YoeB, the most prevalent type II TA system, is present in a variety of bacterial species. In Staphylococcus aureus, the YefM-YoeB system exists as two independent paralogous copies. Our previous research resolved crystal structures of the two oligomeric states (heterotetramer and heterohexamer-DNA ternary complex) of the first paralog as well as the molecular mechanism of transcriptional autoregulation of this module. However, structural details reflecting molecular diversity in both paralogs have been relatively unexplored. To understand the molecular mechanism of how Sa2YoeB and Sa2YefM regulate their own transcription and how each paralog functions independently, we solved a series of crystal structures of the Sa2YoeB-Sa2YefM. Our structural and biochemical data demonstrated that both paralogous copies adopt similar mechanisms of transcriptional autoregulation. In addition, structural analysis suggested that molecular diversity between the two paralogs might be reflected in the interaction profile of YefM and YoeB and the recognition pattern of promoter DNA by YefM. Interaction analysis revealed unique conformational and activating force effected by the interface between Sa2YoeB and Sa2YefM. In addition, the recognition pattern analysis demonstrated that residues Thr7 and Tyr14 of Sa2YefM specifically recognizes the flanking sequences (G and C) of the promoter DNA. Together, these results provide the structural insights into the molecular diversity and independent function of the paralogous copies of the YoeB-YefM TA system.
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Affiliation(s)
- Lu Xue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
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25
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Bellet V, Roger F, Krasteva D, Gouveia T, Drakulovski P, Pottier C, Bertout S. Multilocus sequence typing of strains from the Cryptococcus gattii species complex from different continents. Mycoses 2021; 65:88-96. [PMID: 34726802 DOI: 10.1111/myc.13389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/27/2023]
Abstract
BACKGROUND Cryptococcus neoformans and Cryptococcus gattii species complexes are pathogens causing cryptococcal meningitis, a fungal infection that leads to death unless treated. Worldwide, it is estimated to kill over 180,000 individuals annually. OBJECTIVES We aim to investigate the molecular diversity of C. gattii isolates from strains isolated from 1995 to the present day from different continents. METHOD In this study, we analysed the molecular diversity by MLST and antifungal susceptibility by using the broth microdilution method according to the CLSI M27-A4 protocol of a total of 26 strains from Cryptococcus gattii species complex from both clinical and environmental sources. RESULTS Genotyping showed that most of the strains (17/26; 65.4%) belonged to serotype B and were distributed between three genotypes: VGI (13/17; 76.5%), VGII (3/17; 17.6%) and VGVI (1/17; 5.9%). The serotype C strains (9/26; 34.6%) were distributed between the VGIII (1/9; 11.1%) and VGIV (8/9; 88.9%) genotypes. The 26 strains belonged to 17 different MLST subtypes, and we highlight four new MLST genotypes (ST553, 554, 555 and 556). The two environmental strains were identified as serotype B and genotype VGI, but were of ST 51 and 154. All isolates have wild-type MIC of fluconazole and flucytosine. Regarding amphotericin B, five VGI strains showed MICs to AMB equal to 1 µg/ml, and according to the ECV for these genotypes, they were considered non-wild-type strains. CONCLUSIONS The current study reveals the genetic diversity and new sequence types among strains from the C. gattii complex species.
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Affiliation(s)
- Virginie Bellet
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Frédéric Roger
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Donika Krasteva
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Tiphany Gouveia
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Pascal Drakulovski
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Cyril Pottier
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
| | - Sébastien Bertout
- UMI 233 IRD-UM INSERM U1175 TransVIHMI, Infections mycosiques et parasitaires liées au VIH, Laboratoire de Parasitologie et de Mycologie Médicale, UFR Pharmacie, Montpellier, France
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Gonçalves IL, das Neves GM, Kagami LP, Gonçalves GA, Davi L, Eifler-Lima VL. Exploring the N1 Position of Biginelli Compounds: New Insights and Trends for Chemical Diversity Generation of Bioactive Derivatives. Mini Rev Med Chem 2021; 22:1545-1558. [PMID: 34711161 DOI: 10.2174/1389557521666211027105534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/13/2021] [Accepted: 08/05/2021] [Indexed: 11/22/2022]
Abstract
Dihydropyrimidinones (DHPMs) are heterocycles obtained by the multicomponent Biginelli reaction. Recently, new synthetic protocols have allowed us to explore functionalisation at less explored positions of DHPMs, such as the N1 position. In this context, we have performed a full literature survey of N1-substituted DHPMs. We analysed 27 papers and identified 379 compounds with substituents at the N1 position, most of them with alkyl groups, and of 28% with aromatic substituents attached at the N1 position. N1-substituted DHPMs are explored mainly due to their effects on cancer cell proliferation via numerous targets, such as kinesin Eg5, heat shock protein 70, heat shock protein 90 and the epidermal growth factor receptor. Similarity analyses were performed using the data of 379 DHPMs from different cheminformatic approaches, i.e. chemical property correlations, principal component analysis, similarity networks and compound clustering.
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Affiliation(s)
- Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Guilherme Arraché Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Leonardo Davi
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
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Maceda A, Reyes-Rivera J, Soto-Hernández M, Terrazas T. Distribution and Chemical Composition of Lignin in Secondary Xylem of Cactaceae. Chem Biodivers 2021; 18:e2100431. [PMID: 34496126 DOI: 10.1002/cbdv.202100431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/30/2021] [Indexed: 11/07/2022]
Abstract
Cactaceae family has heterogeneity in the accumulation of lignocellulose due to the diversity of shapes and anatomy of the wood. Most studies focus on fibrous and dimorphic species; but the non-fibrous species are poorly studied. The aims of this work were to analyze the syringyl/guaiacyl ratio of lignin and its distribution in secondary xylem, especially in non-fibrous species. The syringyl/guaiacyl (S/G) ratio was quantified from 34 species of cacti by nitrobenzene oxidation of free-extractive wood. The distribution of lignocellulose in wood sections stained with safranin O/fast green was determined with epifluorescence microscopy. The S/G ratio was heterogeneous; most of the non-fibrous species had a higher percentage of syringyl, while the fibrous ones accumulate guaiacyl. Fluorescence emission showed that vessel elements and wide-band tracheids had similar tonalities. It is hypothesized that the presence of a higher percentage of syringyl in most cacti is part of the defense mechanism against pathogens, which together with the succulence of the stem represent adaptations that contribute to survival in their hostile environments.
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Affiliation(s)
- Agustín Maceda
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Estado de México, 56230, Mexico
| | - Jorge Reyes-Rivera
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, UNAM, Mexico City, 09230, Mexico
| | - Marcos Soto-Hernández
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Estado de México, 56230, Mexico
| | - Teresa Terrazas
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
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28
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Vogt JC, Olefeld JL, Bock C, Boenigk J, Albach DC. Patterns of protist distribution and diversification in alpine lakes across Europe. Microbiologyopen 2021; 10:e1216. [PMID: 34459549 PMCID: PMC8311734 DOI: 10.1002/mbo3.1216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Biogeography in Europe is known to be crucially influenced by the large mountain ranges serving as biogeographical islands for cold‐adapted taxa and geographical barriers for warm‐adapted taxa. While biogeographical patterns are well‐known for plants and animals in Europe, we here investigated diversity and distribution patterns of protist freshwater communities on a European scale (256 lakes) in the light of the well‐studied post‐glacial distribution patterns of macroorganisms. Thus, our study compared 43 alpine protist communities of lakes located in the Alps, Carpathians, Pyrenees, and the Sierra Nevada with that of surrounding lowland lakes. We verified altitudinal diversity gradients of freshwater protists with decreasing richness and diversity across altitudes similar to those observed for plants and animals. Alpine specialists and generalists could be identified differing significantly in richness and diversity, but hardly in occurrence and proportions of major taxonomic groups. High proportions of region‐specific alpine specialists indicate an increased occurrence of distinct lineages within each mountain range and thus, suggested either separated glacial refugia or post‐glacial diversification within mountain ranges. However, a few alpine specialists were shared between mountain ranges suggesting a post‐glacial recolonization from a common lowland pool. Our results identified generalists with wide distribution ranges and putatively wide tolerance ranges toward environmental conditions as main drivers of protist diversification (specification) in alpine lakes, while there was hardly any diversification in alpine specialists.
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Affiliation(s)
- Janina C Vogt
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl von Ossietzky University, Oldenburg, Germany
| | - Jana L Olefeld
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Christina Bock
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Dirk C Albach
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl von Ossietzky University, Oldenburg, Germany
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Bakayoko Y, Kouakou AM, Kouassi AB, Gomez R, Dibi KEB, Essis BS, N’Zué B, Adebola P, N’Guetta AS, Umber M. Detection and diversity of viruses infecting African yam ( Dioscorea rotundata) in a collection and F 1 progenies in Côte d'Ivoire shed light to plant-to-plant viral transmission. Plant Pathol 2021; 70:1486-1495. [PMID: 34413548 PMCID: PMC8360134 DOI: 10.1111/ppa.13393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 05/03/2023]
Abstract
Yam (Dioscorea spp.) is a major staple food whose production is hampered by viral diseases. However, the prevalence, diversity, transmission, and impact of yam-infecting viruses remain poorly documented. This study reports on the symptomatology, prevalence, and molecular diversity of eight viruses in 38 D. rotundata accessions from a germplasm collection and 206 F1 hybrid progenies maintained in Côte d'Ivoire. Mean severity scores as assessed from leaf symptoms ranged from 2 to 4 in the germplasm collection and from 1 to 3 in F1 hybrids, respectively. Dioscorea mosaic-associated virus (DMaV), potexviruses, and yam mosaic virus (YMV) were detected by PCR-based diagnosis tools in single and mixed infections in both the D. rotundata collection and F1 progenies, whereas badnaviruses were detected only in the germplasm collection. In contrast, cucumber mosaic virus (CMV), yam macluraviruses, yam asymptomatic virus 1 (YaV1), and yam mild mosaic virus (YMMV) could not be detected. No correlation could be established between severity scores and indexing results. Phylogenetic analysis performed on partial viral sequences amplified from infected samples unveiled the presence of two putative novel viral species belonging to genera Badnavirus and Potexvirus and provided evidence for plant-to-plant transmission of YMV, DMaV, and yam potexviruses.
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Affiliation(s)
- Yacouba Bakayoko
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Amani M. Kouakou
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Abou B. Kouassi
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Rose‐Marie Gomez
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
| | - Konan E. B. Dibi
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Brice S. Essis
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Boni N’Zué
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Patrick Adebola
- International Institut of Tropical AgricultureIITA‐Abuja StationAbujaNigeria
| | - Assanvon S.‐P. N’Guetta
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Marie Umber
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
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Zhang SX, Carmena D, Ballesteros C, Yang CL, Chen JX, Chu YH, Yu YF, Wu XP, Tian LG, Serrano E. Symptomatic and Asymptomatic Protist Infections in Hospital Inpatients in Southwestern China. Pathogens 2021; 10:684. [PMID: 34072858 DOI: 10.3390/pathogens10060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 12/25/2022] Open
Abstract
Cryptosporidium spp., Entamoeba histolytica, Giardia duodenalis, and Blastocystis sp. infections have been frequently reported as etiological agents for gastroenteritis, but also as common gut inhabitants in apparently healthy individuals. Between July 2016 and March 2017, stool samples (n = 507) were collected from randomly selected individuals (male/female ratio: 1.1, age range: 38–63 years) from two sentinel hospitals in Tengchong City Yunnan Province, China. Molecular (PCR and Sanger sequencing) methods were used to detect and genotype the investigated protist species. Carriage/infection rates were: Blastocystis sp. 9.5% (95% CI: 7.1–12.4%), G. duodenalis 2.2% (95% CI: 1.1–3.8%); and E. histolytica 2.0% (95% CI: 0.9–3.6%). Cryptosporidium spp. was not detected at all. Overall, 12.4% (95% CI: 9.7–15.6) of the participants harbored at least one enteric protist species. The most common coinfection was E. histolytica and Blastocystis sp. (1.0%; 95% CI: 0.3–2.2). Sequence analyses revealed that 90.9% (10/11) of the genotyped G. duodenalis isolates corresponded to the sub-assemblage AI. The remaining sequence (9.1%, 1/11) was identified as sub-assemblage BIV. Five different Blastocystis subtypes, including ST3 (43.7%, 21/48), ST1 (27.1%, 13/48), ST7 (18.8%, 9/48), ST4 (8.3%, 4/48), and ST2 (2.1%, 1/48) were identified. Statistical analyses confirmed that (i) the co-occurrence of protist infections was purely random, (ii) no associations were observed among the four protist species found, and (iii) neither their presence, individually or jointly, nor the patient’s age was predictors for developing clinical symptoms associated with these infections. Overall, these protist mono- or coinfections are asymptomatic and do not follow any pattern.
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Goulas A, Changeux JP, Wagstyl K, Amunts K, Palomero-Gallagher N, Hilgetag CC. The natural axis of transmitter receptor distribution in the human cerebral cortex. Proc Natl Acad Sci U S A 2021; 118:e2020574118. [PMID: 33452137 DOI: 10.1073/pnas.2020574118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Communication between cells in the brain relies on different types of transmitter receptors. Can we uncover organizational principles that harness the diversity of such signatures across the brain? We focus on the human cerebral cortex and demonstrate that the distribution of receptors forms a natural axis that stretches from association to sensory areas. Moreover, traversing this axis entails changes in the diversity, excitability, and mirrored density that reflect a basic division in receptor types, that is, ionotropic and metabotropic receptors. The unraveled principles offer explanatory depth for diverse phenomena and entail concrete, testable predictions. Transmitter receptors constitute a key component of the molecular machinery for intercellular communication in the brain. Recent efforts have mapped the density of diverse transmitter receptors across the human cerebral cortex with an unprecedented level of detail. Here, we distill these observations into key organizational principles. We demonstrate that receptor densities form a natural axis in the human cerebral cortex, reflecting decreases in differentiation at the level of laminar organization and a sensory-to-association axis at the functional level. Along this natural axis, key organizational principles are discerned: progressive molecular diversity (increase of the diversity of receptor density); excitation/inhibition (increase of the ratio of excitatory-to-inhibitory receptor density); and mirrored, orderly changes of the density of ionotropic and metabotropic receptors. The uncovered natural axis formed by the distribution of receptors aligns with the axis that is formed by other dimensions of cortical organization, such as the myelo- and cytoarchitectonic levels. Therefore, the uncovered natural axis constitutes a unifying organizational feature linking multiple dimensions of the cerebral cortex, thus bringing order to the heterogeneity of cortical organization.
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Abstract
The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.
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Affiliation(s)
- Yimin Qiu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chenxi Zhai
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Ling Chen
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Xiaoyan Liu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
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Sandin MM, Biard T, Romac S, O'Dogherty L, Suzuki N, Not F. A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria). Protist 2021; 172:125806. [PMID: 34174720 DOI: 10.1016/j.protis.2021.125806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments, displaying an excellent fossil record extremely valuable for paleo-environmental reconstruction studies, from where most of their extant diversity and ecology have been inferred. This study represents a comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high classification ranks. Such reconsideration allows gathering different morphologies with concentric structure and spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Our calibrated molecular clock dates the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), among the first radiolarian representatives in the fossil record. This study allows a direct connection between living specimens and extinct morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction analysis.
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Stavridou E, Lagiotis G, Kalaitzidou P, Grigoriadis I, Bosmali I, Tsaliki E, Tsiotsiou S, Kalivas A, Ganopoulos I, Madesis P. Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis. Plants (Basel) 2021; 10:656. [PMID: 33808174 DOI: 10.3390/plants10040656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022]
Abstract
A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.
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35
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Gil D, Cardoso JMS, Abrantes I, Esteves I. Pratylenchus penetrans Parasitizing Potato Crops: Morphometric and Genetic Variability of Portuguese Isolates. Plants (Basel) 2021; 10:603. [PMID: 33806880 DOI: 10.3390/plants10030603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
The root lesion Pratylenchus penetrans is an economically important pest affecting a wide range of plants. The morphometry of five P. penetrans isolates, parasitizing potato roots in Portugal, was compared and variability within and between isolates was observed. Of the 15 characters assessed, vulva position (V%) in females and the stylet length in both females/males showed the lowest coefficient of intra and inter-isolate variability. Moreover, DNA sequencing of the internal transcribed spacers (ITS) genomic region and cytochrome c oxidase subunit 1 (COI) gene was performed, in order to evaluate the intraspecific genetic variability of this species. ITS revealed higher isolate genetic diversity than the COI gene, with 15 and 7 different haplotypes from the 15 ITS and 14 COI sequences, respectively. Intra- and inter-isolate genetic diversity was found considering both genomic regions. The differentiation of these isolates was not related with their geographical origin. In spite of the high intraspecific variability, phylogenetic analyses revealed that both ITS region and COI gene separate P. penetrans from other related species. Our findings contribute to increasing the understanding of P. penetrans variability.
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Aoki-Shioi N, Jobichen C, Sivaraman J, Kini RM. Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution. Biochem J 2020; 477:3951-62. [PMID: 33000863 DOI: 10.1042/BCJ20200529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 09/30/2020] [Indexed: 11/17/2022]
Abstract
Snake venoms are complex mixtures of enzymes and nonenzymatic proteins that have evolved to immobilize and kill prey animals or deter predators. Among them, three-finger toxins (3FTxs) belong to the largest superfamily of nonenzymatic proteins. They share a common structure of three β-stranded loops extending like fingers from a central core containing all four conserved disulfide bonds. Most 3FTxs are monomers and through subtle changes in their amino acid sequences, they interact with different receptors, ion channels and enzymes to exhibit a wide variety of biological effects. The 3FTxs have further expanded their pharmacological space through covalent or noncovalent dimerization. Synergistic-type toxins (SynTxs) isolated from the deadly mamba venoms, although nontoxic, have been known to enhance the toxicity of other venom proteins. However, the details of three-dimensional structure and molecular mechanism of activity of this unusual class of 3FTxs are unclear. We determined the first three-dimensional structure of a SynTx isolated from Dendroaspis jamesoni jamesoni (Jameson's mamba) venom. The SynTx forms a unique homodimer that is held together by an interchain disulfide bond. The dimeric interface is elaborate and encompasses loops II and III. In addition to the inter-subunit disulfide bond, the hydrogen bonds and hydrophobic interactions between the monomers contribute to the dimer formation. Besides, two sulfate ions that mediate interactions between the monomers. This unique quaternary structure is evolved through noncovalent homodimers such as κ-bungarotoxins. This novel dimerization further enhances the diversity in structure and function of 3FTxs.
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Zhang M, Shi Z, Yang M, Lu S, Cao L, Wang X. Molecular Diversity and Distribution of Arbuscular Mycorrhizal Fungi at Different Elevations in Mt. Taibai of Qinling Mountain. Front Microbiol 2021; 12:609386. [PMID: 33746912 PMCID: PMC7974767 DOI: 10.3389/fmicb.2021.609386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/01/2021] [Indexed: 01/20/2023] Open
Abstract
Arbuscular mycorrhizal fungi (AMFs) play a vital role in ecosystems, especially in ecosystem variability, diversity, and function. Understanding the AMF diversity, distribution, and their driver at different altitudinal gradients is a benefit for understanding the ecological function of AMF in mountain ecosystems. In this study, we explored the AMF molecular diversity and their distribution from 660 to 3,500 m a.s.l. in Mount Taibai of Qinling Mountains based on high-throughput sequencing technology. A total of 702 operational taxonomic units (OTUs) in 103 species of AMF are isolated from soil samples, which belong to 18 identified and 1 unidentified genus in 10 families. The fungi in the genus of Glomus is the most dominant, with the occurrence frequency of 100% and the relative abundance of 42.268% and 33.048% on the species and OTU level, respectively. The AMF colonization in root could be simulated by a cubic function with the change of altitudes with the peak and trough at a.s.l. 1,170 and 2,850 m, respectively. Further, AMF diversity indices including Sob, Shannon diversity, and Pielou evenness also showed the same cubic function change trends with increasing altitude at OTU and species levels. However, the average values of diversity indices at OTU level are always higher than these at the species level. Based on the OTU level, the highest and lowest values of Shannon and Pielou indices are observed at the altitudes of 1,400 and 2,800 m, respectively. The pattern of AMF community distribution in Mt. Taibai is driven by altitude with the characteristics of more abundance in the medium- to low-altitude than high-altitude areas. In general, abundant AMF molecular diversity and species exit in different elevations of Mt. Taibai, which indicate gradient changes with elevations.
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Affiliation(s)
- Mengge Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.,Luoyang Key Laboratory of Symbiotic Microorganism and Green Development, Luoyang, China.,Henan Engineering Research Center of Human Settlements, Luoyang, China
| | - Zhaoyong Shi
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.,Luoyang Key Laboratory of Symbiotic Microorganism and Green Development, Luoyang, China.,Henan Engineering Research Center of Human Settlements, Luoyang, China
| | - Mei Yang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.,Luoyang Key Laboratory of Symbiotic Microorganism and Green Development, Luoyang, China.,Henan Engineering Research Center of Human Settlements, Luoyang, China
| | - Shichuan Lu
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.,Luoyang Key Laboratory of Symbiotic Microorganism and Green Development, Luoyang, China.,Henan Engineering Research Center of Human Settlements, Luoyang, China
| | - Libing Cao
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Xugang Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.,Luoyang Key Laboratory of Symbiotic Microorganism and Green Development, Luoyang, China.,Henan Engineering Research Center of Human Settlements, Luoyang, China
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McCosker PM, Butler NM, Shakoori A, Volland MK, Perry MJ, Mullen JW, Willis AC, Clark T, Bremner JB, Guldi DM, Keller PA. The Cascade Reactions of Indigo with Propargyl Substrates for Heterocyclic and Photophysical Diversity. Chemistry 2021; 27:3708-3721. [PMID: 32885487 DOI: 10.1002/chem.202003662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/31/2020] [Indexed: 11/11/2022]
Abstract
The synthesis of structurally diverse heterocycles for chemical space exploration was achieved via the cascade reactions of indigo with propargylic electrophiles. New pyrazinodiindolodione, naphthyridinedione, azepinodiindolone, oxazinoindolone and pyrrolodione products were prepared in one pot reactions by varying the leaving group (-Cl, -Br, -OMs, -OTs) or propargyl terminal functionality (-H, -Me, -Ph, -Ar). Mechanistic and density functional theory studies revealed that the unsaturated propargyl moiety can behave as an electrophile when aromatic terminal substitutions are made, and therefore competes with leaving group substitution for new outcomes. Selected products from the cascade reactions were investigated for their absorption and fluorescence properties, including transient absorption spectroscopy. This revealed polarity dependent excited state relaxation pathways, fluorescence, and triplet formation, thus highlighting these reactions as a means to access diverse functional materials rapidly.
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Affiliation(s)
- Patrick M McCosker
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia.,Department of Chemistry and Pharmacy, Computer-Chemistry-Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelbachstrasse 25, 91052, Erlangen, Germany.,Department of Chemistry and Pharmacy, Interdisciplinary Center for Molecular Materials (ICMM), Chair of Physical Chemistry I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstrasse 3, 91058, Erlangen, Germany
| | - Nicholas M Butler
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
| | - Alireza Shakoori
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
| | - Michel K Volland
- Department of Chemistry and Pharmacy, Interdisciplinary Center for Molecular Materials (ICMM), Chair of Physical Chemistry I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstrasse 3, 91058, Erlangen, Germany
| | - Matthew J Perry
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
| | - Jesse W Mullen
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
| | - Anthony C Willis
- Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelbachstrasse 25, 91052, Erlangen, Germany
| | - John B Bremner
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
| | - Dirk M Guldi
- Department of Chemistry and Pharmacy, Interdisciplinary Center for Molecular Materials (ICMM), Chair of Physical Chemistry I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstrasse 3, 91058, Erlangen, Germany
| | - Paul A Keller
- School of Chemistry & Molecular Bioscience, Molecular Horizons, Illawarra Health & Medical Research Institute, University of Wollongong, Northfields Avenue, 2522, Wollongong, NSW, Australia
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Wen S, Wang G, Yang Z, Wang Y, Rao M, Lu Q, Hong N. Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China. Front Microbiol 2020; 11:602039. [PMID: 33391218 PMCID: PMC7774462 DOI: 10.3389/fmicb.2020.602039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.
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Affiliation(s)
- Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Rao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Lu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
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40
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Al-Sheikh A, Begum M, Zhang B, Lewis RA, Allenby NEE, Waddell PG, Golding BT. Molecular Diversity via Tetrasubstituted Alkenes Containing a Barbiturate Motif: Synthesis and Biological Activity. Molecules 2020; 25:E5868. [PMID: 33322563 DOI: 10.3390/molecules25245868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/17/2022] Open
Abstract
The synthesis of a molecularly diverse library of tetrasubstituted alkenes containing a barbiturate motif is described. Base-induced condensation of N1-substituted pyrimidine-2,4,6(1H,3H,5H)-triones with 5-(bis(methylthio)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione gave 3-substituted 5-(methylthio)-2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones (‘pyranopyrimidinones’), regioselectively. A sequence of reactions involving ring-opening of the pyran moiety, displacement of the methylthio group with an amine, re-formation of the pyran ring, and after its final cleavage with an amine, gave tetrasubstituted alkenes (3-amino-3-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)propanamides) with a diversity of substituents. Cleavage of the pyranopyrimidinones with an aniline was facilitated in 2,2,2-trifluoroethanol under microwave irradiation. Compounds were tested against Escherichia coli, Staphylococcus aureus, the yeast Schizosaccharomyces pombe, and the pathogenic fungus Candida albicans. No compounds exhibited activity against E. coli, whilst one compound was weakly active against S. aureus. Three compounds were strongly active against S. pombe, but none was active against C. albicans.
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41
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Ziarani GM, Mohajer F, Mali SN. The molecular diversity of 1,8-diaminonaphthalene in organic chemistry. Comb Chem High Throughput Screen 2020; 24:1702-1713. [PMID: 33172368 DOI: 10.2174/1386207323666201110144014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 11/22/2022]
Abstract
1,8-diaminonaphthalene (1,8-DAN) with special organic structure was applied in organic synthesis to provide efficient complex scaffolds, through the two or four-component fashion. This review highlights its recent application in organic reactions under different conditions and heterogynous catalysts to produce various molecules, which were used as medicines, sensors, and dyes.
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Affiliation(s)
- Ghodsi Mohammadi Ziarani
- Department of Physics and Chemistry, Faculty of Science, University of Alzahra, Vanak Square, 1993893973, Tehran. Iran
| | - Fatemeh Mohajer
- Department of Physics and Chemistry, Faculty of Science, University of Alzahra, Vanak Square, 1993893973, Tehran. Iran
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Badarau E, Reddy KHV, Loudet A, Simon C, Trembleau L, Claerhout S, Pair E, Massip S, Breton P, Lesur B, Goldstein S, Fourquez JM, Henlin JM, Ghosez L. Productive Syntheses of Privileged Scaffolds Inspired by the Recognition of a Diels-Alder Pattern Common to Three Classes of Natural Products. Chemistry 2020; 26:15477-15481. [PMID: 32428343 DOI: 10.1002/chem.202002372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 11/10/2022]
Abstract
Identification of a common Diels-Alder pattern in three classes of bioactive natural products led us to study the synthesis and cycloaddition of a new class of cyclic dienes readily available from β,γ-unsaturated lactams. A practical and readily scalable route to the parent p-methoxybenzyl-protected 6- and 7-membered β,γ-unsaturated lactams was developed. These were readily transformed into the corresponding O-silylated dienes, which were reacted with dimethyl and diethyl fumarate to yield stereoselectively highly functionalized bicyclic adducts. These exhibited unexpected and versatile transformations upon acid hydrolysis depending on the nature of the dienophile substituents and the acid catalyst. All reactions have been performed on multigram quantities. These transformations provide a convenient, economical, and easily scalable pathway for the rapid construction of functionally and stereochemically dense privileged scaffolds for the construction of libraries of natural products-inspired molecules of pharmacological relevance.
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Affiliation(s)
- Eduard Badarau
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France.,Bordeaux INP, CNRS UMR 5248, Université de Bordeaux, CBMN, Allée Geoffroy Saint Hilaire, Bat B14, 33600, Pessac, France
| | - K Harsha Vardhan Reddy
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Aurore Loudet
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Charles Simon
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Laurent Trembleau
- UCLouvain, Place Louis Pasteur 1, 1348, Louvain-la-Neuve, Belgium.,Chemistry, G95, School of Natural and Computing Sciences, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Stijn Claerhout
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Etienne Pair
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Stéphane Massip
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France
| | - Philippe Breton
- Institut de Recherche Servier, 125, chemin de Ronde, 78290, Croissy Sur Seine, France
| | - Brigitte Lesur
- Institut de Recherche Servier, 125, chemin de Ronde, 78290, Croissy Sur Seine, France
| | - Solo Goldstein
- Institut de Recherche Servier, 125, chemin de Ronde, 78290, Croissy Sur Seine, France
| | - Jean-Marie Fourquez
- Institut de Recherche Servier, 125, chemin de Ronde, 78290, Croissy Sur Seine, France
| | - Jean Michel Henlin
- Institut de Recherche Servier, 125, chemin de Ronde, 78290, Croissy Sur Seine, France
| | - Léon Ghosez
- IECB, CNRS UMR 5248, Université de Bordeaux, CBMN, 2, rue Robert Escarpit, 33607, Pessac, France.,UCLouvain, Place Louis Pasteur 1, 1348, Louvain-la-Neuve, Belgium
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Karageorgis G, Liver S, Nelson A. Activity-Directed Synthesis: A Flexible Approach for Lead Generation. ChemMedChem 2020; 15:1776-1782. [PMID: 32734671 PMCID: PMC7589241 DOI: 10.1002/cmdc.202000524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 11/06/2022]
Abstract
Activity‐directed synthesis (ADS) is a structure‐blind, functional‐driven molecular discovery approach. In this Concept, four case studies highlight the general applicability of ADS and showcase its flexibility to support different medicinal chemistry strategies. ADS deliberately harnesses reactions with multiple possible outcomes, and allows many chemotypes to be evaluated in parallel. Resources are focused on bioactive molecules, which emerge in tandem with associated synthetic routes. Some of the future challenges for ADS are highlighted, including the realisation of an autonomous molecular discovery platform. The prospects for ADS to become a mainstream lead generation approach are discussed.
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Affiliation(s)
- George Karageorgis
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Samuel Liver
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, UK
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, UK
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44
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Arroyo AS, Lannes R, Bapteste E, Ruiz-Trillo I. Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition. Genome Biol Evol 2020; 12:1664-1678. [PMID: 32533833 PMCID: PMC7533066 DOI: 10.1093/gbe/evaa117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
The Holozoa clade comprises animals and several unicellular lineages (choanoflagellates, filastereans, and teretosporeans). Understanding their full diversity is essential to address the origins of animals and other evolutionary questions. However, they are poorly known. To provide more insights into the real diversity of holozoans and check for undiscovered diversity, we here analyzed 18S rDNA metabarcoding data from the global Tara Oceans expedition. To overcome the low phylogenetic information contained in the metabarcoding data set (composed of sequences from the short V9 region of the gene), we used similarity networks by combining two data sets: unknown environmental sequences from Tara Oceans and known reference sequences from GenBank. We then calculated network metrics to compare environmental sequences with reference sequences. These metrics reflected the divergence between both types of sequences and provided an effective way to search for evolutionary relevant diversity, further validated by phylogenetic placements. Our results showed that the percentage of unicellular holozoan diversity remains hidden. We found novelties in several lineages, especially in Acanthoecida choanoflagellates. We also identified a potential new holozoan group that could not be assigned to any of the described extant clades. Data on geographical distribution showed that, although ubiquitous, each unicellular holozoan lineage exhibits a different distribution pattern. We also identified a positive association between new animal hosts and the ichthyosporean symbiont Creolimax fragrantissima, as well as for other holozoans previously reported as free-living. Overall, our analyses provide a fresh perspective into the diversity and ecology of unicellular holozoans, highlighting the amount of undescribed diversity.
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Affiliation(s)
- Alicia S Arroyo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Romain Lannes
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Departament de Genètica, Microbiologia I Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Spain
- ICREA, Barcelona, Spain
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45
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Green AI, Hobor F, Tinworth CP, Warriner S, Wilson AJ, Nelson A. Activity-Directed Synthesis of Inhibitors of the p53/hDM2 Protein-Protein Interaction. Chemistry 2020; 26:10682-10689. [PMID: 32458465 PMCID: PMC7496268 DOI: 10.1002/chem.202002153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/10/2023]
Abstract
Protein–protein interactions (PPIs) provide a rich source of potential targets for drug discovery and biomedical science research. However, the identification of structural‐diverse starting points for discovery of PPI inhibitors remains a significant challenge. Activity‐directed synthesis (ADS), a function‐driven discovery approach, was harnessed in the discovery of the p53/hDM2 PPI. Over two rounds of ADS, 346 microscale reactions were performed, with prioritisation on the basis of the activity of the resulting product mixtures. Four distinct and novel series of PPI inhibitors were discovered that, through biophysical characterisation, were shown to have promising ligand efficiencies. It was thus shown that ADS can facilitate ligand discovery for a target that does not have a defined small‐molecule binding site, and can provide distinctive starting points for the discovery of PPI inhibitors.
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Affiliation(s)
- Adam I Green
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | | | - Stuart Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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46
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Mamontov A, Martin-Mingot A, Métayer B, Karam O, Zunino F, Bouazza F, Thibaudeau S. Complementary Site-Selective Halogenation of Nitrogen-Containing (Hetero)Aromatics with Superacids. Chemistry 2020; 26:10411-10416. [PMID: 32212405 DOI: 10.1002/chem.202000902] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 12/11/2022]
Abstract
Site-selective functionalization of arenes that is complementary to classical aromatic substitution reactions remains a long-standing quest in organic synthesis. Exploiting the generation of halenium ion through oxidative process and the protonation of the nitrogen containing function in HF/SbF5 , the chlorination and iodination of classically inert Csp2 -H bonds of aromatic amines occurs. Furthermore, the superacid-promoted (poly)protonation of the molecules acts as a protection, favoring the late-stage selective halogenation of natural alkaloids and active pharmaceutical ingredients.
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Affiliation(s)
- Alexander Mamontov
- Université de Poitiers, UMR-CNRS 7285, IC2MP, Superacid Group - Organic Synthesis Team, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 9, France.,@rtMolecule, 1 rue Georges Bonnet, Bâtiment B37, 86000, Poitiers, France
| | - Agnès Martin-Mingot
- Université de Poitiers, UMR-CNRS 7285, IC2MP, Superacid Group - Organic Synthesis Team, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Benoit Métayer
- Université de Poitiers, UMR-CNRS 7285, IC2MP, Superacid Group - Organic Synthesis Team, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 9, France.,@rtMolecule, 1 rue Georges Bonnet, Bâtiment B37, 86000, Poitiers, France
| | - Omar Karam
- @rtMolecule, 1 rue Georges Bonnet, Bâtiment B37, 86000, Poitiers, France
| | - Fabien Zunino
- @rtMolecule, 1 rue Georges Bonnet, Bâtiment B37, 86000, Poitiers, France
| | - Fodil Bouazza
- @rtMolecule, 1 rue Georges Bonnet, Bâtiment B37, 86000, Poitiers, France
| | - Sébastien Thibaudeau
- Université de Poitiers, UMR-CNRS 7285, IC2MP, Superacid Group - Organic Synthesis Team, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 9, France
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening. Angew Chem Int Ed Engl 2020; 59:14809-14817. [PMID: 32363632 DOI: 10.1002/anie.202002463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.
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Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Regis Denay
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Christelle Henry
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas O Frank
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
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Abstract
Around the world, the number of compound databases of natural products in the public domain is rising. This is in line with the increasing synergistic combination of natural product research and chemoinformatics. Toward this global endeavor, countries in Latin America are assembling, curating, and analyzing the contents and diversity of natural products available in their geographical regions. In this manuscript we collect and analyze the efforts that countries in Latin America have made so far to build natural product databases. We further encourage the scientific community in particular in Latin America, to continue their efforts to building quality natural product databases and, whenever possible, to make them publicly accessible. It is proposed that all compound collections could be assembled into a unified resource called LANaPD: Latin American Natural Products Database. Opportunities and challenges to build, distribute and maintain LANaPD are also discussed. Due to the importance of natural products in drug discovery and other areas of science, research groups are building and maintaining compound databases of natural products. This report analyzes the compounds databases developed and published, thus far by Latin American countries and proposes the creation of a unified resource named LANaPD: Latin American Natural Products Database. The generation, curation, analysis, distribution and maintenance of LANaPD will require joint efforts from different countries. Such a goal is not straightforward and simple but it is possible and will be useful. In this report the benefits and challenges of creating LANaPD are discussed.
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Yakunin E, Kostyal E, Agmon V, Grotto I, Valinsky L, Moran-Gilad J. A Snapshot of the Prevalence and Molecular Diversity of Legionella pneumophila in the Water Systems of Israeli Hotels. Pathogens 2020; 9:pathogens9060414. [PMID: 32471136 PMCID: PMC7350324 DOI: 10.3390/pathogens9060414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 11/16/2022] Open
Abstract
Exposure to Legionella spp. contaminated aerosols in hotel settings confers risk for travel-associated Legionnaire’s disease (TALD). In this study, we investigated the prevalence of Legionella contamination and its molecular diversity in hotels and resorts across Israel. The study was comprised of a convenience sample of water systems from 168 hotels and resorts countrywide, routinely inspected between March 2015 and February 2017. Isolation and quantitation of Legionella were performed in a water laboratory using the ISO 11731 method. The distribution of Legionella isolates was analyzed according to geography and source. The genetic diversity of a subset of isolates was analyzed by sequence-based typing (SBT) at the National Reference Laboratory for Legionella and compared to the national database. Out of 2830 samples tested, 470 (17%) obtained from 102 different premises (60% of hotels) were positive for Legionella spp. In 230 samples (49% of all positive, 8% of total samples), accounting for 37% of hotels, Legionella spp. counts exceeded the regulatory threshold of 1000 CFU/L. The most frequently contaminated water sources were cooling towers (38%), followed by faucets, hot tubs, water lines, and storage tanks (14–17% each). Furthermore, 32% and 17% of samples obtained from cooling towers and hot tubs, respectively, exceeded the regulatory thresholds. SBT was performed on 78 strains and revealed 27 different sequence types (STs), including two novel STs. The most prevalent STs found were ST1 (26%), ST87 (10%), ST93 (6%), and ST461 and ST1516 (5% each). Several L. pneumophila STs were found to be limited to certain geographical regions. This is the first study to investigate the prevalence and diversity of Legionella in hotels and resorts in Israel during non-outbreak environmental inspections. These findings will inform risk assessment, surveillance, and control measures of TALD.
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Affiliation(s)
- Eugenia Yakunin
- Central Laboratories and Public Health Services, Ministry of Health, Jerusalem 9134302, Israel; (E.Y.); (V.A.); (I.G.); (L.V.)
| | - Eszter Kostyal
- Department of Water Microbiology, Biolab Ltd., Jerusalem 9134001, Israel;
| | - Vered Agmon
- Central Laboratories and Public Health Services, Ministry of Health, Jerusalem 9134302, Israel; (E.Y.); (V.A.); (I.G.); (L.V.)
| | - Itamar Grotto
- Central Laboratories and Public Health Services, Ministry of Health, Jerusalem 9134302, Israel; (E.Y.); (V.A.); (I.G.); (L.V.)
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Lea Valinsky
- Central Laboratories and Public Health Services, Ministry of Health, Jerusalem 9134302, Israel; (E.Y.); (V.A.); (I.G.); (L.V.)
| | - Jacob Moran-Gilad
- Central Laboratories and Public Health Services, Ministry of Health, Jerusalem 9134302, Israel; (E.Y.); (V.A.); (I.G.); (L.V.)
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence:
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50
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Cobo-Díaz JF, Baroncelli R, Le Floch G, Picot A. A novel metabarcoding approach to investigate Fusarium species composition in soil and plant samples. FEMS Microbiol Ecol 2020; 95:5513441. [PMID: 31183494 DOI: 10.1093/femsec/fiz084] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
The genus Fusarium contains more than 300 species, most of which are plant pathogens. Appropriate molecular tools for accurately and rapidly describing temporal and spatial shifts in Fusarium communities would be useful for the development of control strategies. Here, we present a new Fusarium-specific primer pair targeting the translation elongation factor 1-α (EF1α) gene with amplicons of ~430 bp, suitable for MiSeq metabarcoding sequencing. Mock Fusarium communities were used to evaluate its resolution and to optimize read filtering and downstream analyses. The use of the DADA2 pipeline coupled with operational taxonomic unit (OTU) picking at 98% similarity cut-off significantly increased the accuracy of read filtering. Building a phylogenetic tree using a manually curated database as a reference allowed taxonomic assignment at the species or species-complex level. This methodology was tested on soil and maize residue samples collected from crop fields. Up to 18 Fusarium OTUs, belonging to 17 species and 8 species complexes, were obtained, with F. oxysporum being the most abundant species in soil samples, while F. graminearum and F. avenaceum were the most abundant in maize residues. We demonstrated the high performance of this workflow which could be further used for profiling Fusarium species composition and dynamics during the cultivation cycle.
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Affiliation(s)
- José F Cobo-Díaz
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Riccardo Baroncelli
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Calle del Duero 12, 37185 Villamayor (Salamanca), Spain
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280 Plouzané, France
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